Next-generation sequencing identified microRNAs that associate with motile aeromonad septicemia in grass carp

MicroRNAs (miRNAs) modulate many biological processes and can be up-or down-regulated in a variety of diseases states, including in bacterial infection. In this study, we characterized miRNAs associated with susceptibility or resistance to motile Aeromonas hydrophila in grass carp (Ctenopharyngodon idella), a commercially important farmed fish species in China. Using Illumina next-generation sequencing, we detected 185 miRNAs in A. hydrophila-susceptible (SGC) and -resistant grass carp (RGC) during immune activation. Twenty-one miRNAs were found to be differentially expressed between SGC and RGC, with 23.8% (5 out 21) exhibiting elevated expression in SGC. Further investigation of a selected five miRNAs indicated differences in the timing and tissue sources of expression. Target genes likely regulated by these miRNAs were identified using computational prediction combined with transcriptome expression data. MiRNA targets of differentially expressed mRNAs included those with functions important for bacterial resistance, such as tlr4 and nfil3-6. In addition, we demonstrated that nfil3-6 and tlr4 genes are direct targets of let-7i and cid-miRn-118. The present study suggested that the multiple miRNAs, displaying diverse kinetics and tissue sources on antibacterial immune processes.